Journal
BRIEFINGS IN BIOINFORMATICS
Volume 23, Issue 5, Pages -Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bib/bbac363
Keywords
drug-drug interactions; biomedical knowledge graph; graph neural network; deep learning; multi-feature aggregation
Funding
- Science and Technology Innovation 2030-New Generation Artificial Intelligence Major Project [2018AAA0100103]
- National Natural Science Foundation of China [62002297, 61722212, 62072378, 62172338]
- Neural Science Foundation of Shanxi Province [2022JQ-700]
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Prediction of drug-drug interactions (DDIs) is a challenging task in drug development and clinical application. This study proposes a deep learning framework called DeepLGF to improve the performance of DDIs prediction by fully leveraging the local and global information in the biomedical knowledge graph (BKG).
Drug-drug interactions (DDIs) prediction is a challenging task in drug development and clinical application. Due to the extremely large complete set of all possible DDIs, computer-aided DDIs prediction methods are getting lots of attention in the pharmaceutical industry and academia. However, most existing computational methods only use single perspective information and few of them conduct the task based on the biomedical knowledge graph (BKG), which can provide more detailed and comprehensive drug lateral side information flow. To this end, a deep learning framework, namely DeepLGF, is proposed to fully exploit BKG fusing local-global information to improve the performance of DDIs prediction. More specifically, DeepLGF first obtains chemical local information on drug sequence semantics through a natural language processing algorithm. Then a model of BFGNN based on graph neural network is proposed to extract biological local information on drug through learning embedding vector from different biological functional spaces. The global feature information is extracted from the BKG by our knowledge graph embedding method. In DeepLGF, for fusing local-global features well, we designed four aggregating methods to explore the most suitable ones. Finally, the advanced fusing feature vectors are fed into deep neural network to train and predict. To evaluate the prediction performance of DeepLGF, we tested our method in three prediction tasks and compared it with state-of-the-art models. In addition, case studies of three cancer-related and COVID-19-related drugs further demonstrated DeepLGF's superior ability for potential DDIs prediction. The webserver of the DeepLGF predictor is freely available at http://120.77.11.78/DeepLGF/.
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